Contacts of the helix formed by residues 1209 - 1217 (chain F) in PDB entry 6C3P
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY1209 (chain F).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
777F TRP* 3.4 31.2 - - - -
1205F GLU 2.9 10.7 + - - -
1206F THR 3.7 3.4 - - - -
1208F GLU* 1.3 77.3 - - - +
1210F LEU* 1.3 59.5 + - - -
1211F THR* 3.4 3.6 - - - -
1212F THR* 2.6 25.0 + - - -
1213F ILE* 3.1 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1210 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399F ILE* 3.6 31.2 - - + +
400F MET* 4.5 17.9 - - + -
402F LEU* 4.3 17.3 - - + +
404F THR* 5.3 3.1 - - - +
407F LEU* 6.0 2.9 - - + -
1206F THR* 3.1 33.3 + - + +
1207F VAL* 3.4 17.2 + - + +
1208F GLU 3.5 0.8 + - - -
1209F GLY* 1.3 75.4 - - - +
1211F THR* 1.3 62.3 + - + +
1213F ILE* 3.3 6.9 + - + +
1214F ARG* 3.0 56.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1211 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
404F THR* 4.0 15.7 - - + +
724F LEU* 5.4 11.0 - - + -
727F LEU* 5.2 3.4 - - - +
729F GLU* 4.5 10.8 - - + +
771F TYR* 3.9 22.1 + - - -
773F SER* 5.1 2.9 - - - -
1208F GLU 5.7 0.2 + - - -
1209F GLY* 4.9 1.2 - - - -
1210F LEU* 1.3 79.6 + - + +
1212F THR* 1.3 69.1 + - - +
1214F ARG* 3.3 29.3 + - - +
1215F ALA* 2.9 27.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR1212 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771F TYR* 3.4 35.4 - - + +
773F SER* 4.7 10.5 - - - +
777F TRP* 3.4 29.8 - - + -
789F PHE* 6.1 0.5 - - - -
1209F GLY* 2.6 23.5 + - - +
1211F THR* 1.3 84.7 + - - +
1213F ILE* 1.3 67.0 + - - +
1215F ALA* 3.0 3.2 + - - +
1216F PHE* 2.8 44.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1213 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F MET* 4.2 22.2 - - + -
777F TRP* 4.7 7.0 - - + -
789F PHE* 5.2 4.3 - - + -
1205F GLU 4.5 2.9 - - - +
1206F THR* 4.1 26.9 - - + +
1209F GLY 3.1 21.0 + - - +
1210F LEU* 3.3 8.3 + - + +
1212F THR* 1.3 85.4 + - - +
1214F ARG* 1.3 64.7 + - - +
1215F ALA 3.2 0.2 + - - -
1216F PHE* 3.2 6.5 + - - +
1217F ARG* 2.9 19.2 + - - -
1218F TYR* 3.8 7.5 + - + -
1219F GLU* 4.4 13.8 + - - +
1222F PHE* 3.4 45.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1214 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400F MET* 4.6 26.0 + - - +
402F LEU 3.3 16.5 + - - -
404F THR* 2.6 19.5 + - - -
619F ILE* 4.7 18.4 - - - -
729F GLU* 2.4 49.8 + - - +
1210F LEU* 3.0 50.6 + - + +
1211F THR* 3.3 23.9 - - - +
1213F ILE* 1.3 76.8 - - - +
1215F ALA* 1.3 62.4 + - - +
1217F ARG* 3.1 34.3 + - - +
1219F GLU* 5.9 3.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA1215 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727F LEU* 3.8 23.8 - - + -
729F GLU* 5.2 0.4 + - - -
767F GLY 3.9 1.0 - - - +
769F VAL* 3.5 23.5 + - + +
771F TYR* 3.7 27.6 - - + -
1211F THR 2.9 15.1 + - - +
1212F THR 3.0 8.0 + - - +
1214F ARG* 1.3 78.1 - - - +
1216F PHE* 1.3 63.2 + - - +
1217F ARG* 3.0 12.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE1216 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
768F PRO* 3.3 10.8 - - - +
769F VAL 4.0 8.1 - - - -
770F ALA* 3.7 11.4 - - + -
771F TYR* 3.5 27.6 - - + -
789F PHE* 3.2 46.0 - + + -
841F ARG* 4.8 17.0 - - + -
845F GLN* 3.3 41.3 - - + -
1212F THR* 2.8 50.4 + - - +
1213F ILE 3.9 3.1 - - - +
1215F ALA* 1.3 70.3 - - + +
1217F ARG* 1.3 63.5 + - - +
1218F TYR* 3.0 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG1217 (chain F).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
766F ARG* 5.3 13.1 - - + +
767F GLY 3.9 17.7 - - - +
768F PRO* 4.1 9.4 - - + -
1213F ILE 2.9 7.9 + - - -
1214F ARG* 3.1 23.8 + - - +
1215F ALA 3.0 14.7 - - - +
1216F PHE* 1.3 78.1 - - - +
1218F TYR* 1.3 59.7 + - - +
1219F GLU* 3.3 36.3 + - - +
1220F ALA 5.1 0.2 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il